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changeset 16:a69f73853101 draft

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planemo upload for repository https://github.com/tseemann/snippy commit 93b22331ca83a82fdfbe8f2b274577e21f9bf025-dirty
author dfornika
date Tue, 22 Jan 2019 13:52:10 -0500
parents bf6dbc4d4957
children 412683e7a8fe
files snippy_core_wrapper.py
diffstat 1 files changed, 7 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/snippy_core_wrapper.py	Tue Jan 22 13:26:27 2019 -0500
+++ b/snippy_core_wrapper.py	Tue Jan 22 13:52:10 2019 -0500
@@ -27,17 +27,18 @@
 
     snippy_core_command_line = ['snippy-core', '--ref', args.ref]
 
-    for input_datasets in args.input_datasets.split(','):
-        base_name = os.path.basename(indir)
-        copyfile(indir, '.')
+    for input_dataset in args.indirs.split(','):
+        base_name = os.path.basename(input_dataset)
+        print("base_name: " + base_name)
+        copyfile(input_dataset, base_name)
         subprocess.Popen(['tar', '-xf', base_name])
 
     extracted_dirs = [f for f in os.listdir('.') if os.path.isdir(f) ]
-
+    print("extracted_dirs: " + str(extracted_dirs))
     for extracted_dir in extracted_dirs:
         snippy_core_command_line.append(extracted_dir)
-
-    subprocess.Popen(snippy_core_command_line)
+    print(str(snippy_core_command_line))
+    subprocess.Popen(snippy_core_command_line).wait()
 
 if __name__ == '__main__':
     main()